polars-bio 0.13.1__tar.gz → 0.14.0__tar.gz

{polars_bio-0.13.1 → polars_bio-0.14.0}/Cargo.lock

@@ -1404,7 +1404,7 @@ dependencies = [
 [[package]]
 name = "datafusion-bio-format-bam"
 version = "0.1.0"
-source = "git+https://github.com/biodatageeks/datafusion-bio-formats.git?rev=0b9746c77aeb0e3a29f6460cb29f48aa17625c1d#0b9746c77aeb0e3a29f6460cb29f48aa17625c1d"
+source = "git+https://github.com/biodatageeks/datafusion-bio-formats.git?rev=aecd7b316c1c498bff14c2cbb4ac0bd04d21612f#aecd7b316c1c498bff14c2cbb4ac0bd04d21612f"
 dependencies = [
  "async-stream",
  "async-trait",
@@ -1425,7 +1425,7 @@ dependencies = [
 [[package]]
 name = "datafusion-bio-format-bed"
 version = "0.1.0"
-source = "git+https://github.com/biodatageeks/datafusion-bio-formats.git?rev=0b9746c77aeb0e3a29f6460cb29f48aa17625c1d#0b9746c77aeb0e3a29f6460cb29f48aa17625c1d"
+source = "git+https://github.com/biodatageeks/datafusion-bio-formats.git?rev=aecd7b316c1c498bff14c2cbb4ac0bd04d21612f#aecd7b316c1c498bff14c2cbb4ac0bd04d21612f"
 dependencies = [
  "async-compression",
  "async-stream",
@@ -1449,7 +1449,7 @@ dependencies = [
 [[package]]
 name = "datafusion-bio-format-core"
 version = "0.1.0"
-source = "git+https://github.com/biodatageeks/datafusion-bio-formats.git?rev=0b9746c77aeb0e3a29f6460cb29f48aa17625c1d#0b9746c77aeb0e3a29f6460cb29f48aa17625c1d"
+source = "git+https://github.com/biodatageeks/datafusion-bio-formats.git?rev=aecd7b316c1c498bff14c2cbb4ac0bd04d21612f#aecd7b316c1c498bff14c2cbb4ac0bd04d21612f"
 dependencies = [
  "async-compression",
  "bytes",
@@ -1468,7 +1468,7 @@ dependencies = [
 [[package]]
 name = "datafusion-bio-format-fasta"
 version = "0.1.0"
-source = "git+https://github.com/biodatageeks/datafusion-bio-formats.git?rev=0b9746c77aeb0e3a29f6460cb29f48aa17625c1d#0b9746c77aeb0e3a29f6460cb29f48aa17625c1d"
+source = "git+https://github.com/biodatageeks/datafusion-bio-formats.git?rev=aecd7b316c1c498bff14c2cbb4ac0bd04d21612f#aecd7b316c1c498bff14c2cbb4ac0bd04d21612f"
 dependencies = [
  "async-compression",
  "async-stream",
@@ -1490,7 +1490,7 @@ dependencies = [
 [[package]]
 name = "datafusion-bio-format-fastq"
 version = "0.1.0"
-source = "git+https://github.com/biodatageeks/datafusion-bio-formats.git?rev=0b9746c77aeb0e3a29f6460cb29f48aa17625c1d#0b9746c77aeb0e3a29f6460cb29f48aa17625c1d"
+source = "git+https://github.com/biodatageeks/datafusion-bio-formats.git?rev=aecd7b316c1c498bff14c2cbb4ac0bd04d21612f#aecd7b316c1c498bff14c2cbb4ac0bd04d21612f"
 dependencies = [
  "async-compression",
  "async-stream",
@@ -1514,7 +1514,7 @@ dependencies = [
 [[package]]
 name = "datafusion-bio-format-gff"
 version = "0.1.0"
-source = "git+https://github.com/biodatageeks/datafusion-bio-formats.git?rev=0b9746c77aeb0e3a29f6460cb29f48aa17625c1d#0b9746c77aeb0e3a29f6460cb29f48aa17625c1d"
+source = "git+https://github.com/biodatageeks/datafusion-bio-formats.git?rev=aecd7b316c1c498bff14c2cbb4ac0bd04d21612f#aecd7b316c1c498bff14c2cbb4ac0bd04d21612f"
 dependencies = [
  "async-compression",
  "async-stream",
@@ -1523,20 +1523,23 @@ dependencies = [
  "datafusion",
  "datafusion-bio-format-core",
  "env_logger",
+ "flate2",
  "futures",
  "futures-util",
  "log",
  "noodles 0.93.0",
- "noodles-gff 0.50.0",
+ "noodles-bgzf 0.36.0",
+ "noodles-gff 0.51.0",
  "opendal",
  "tokio",
  "tokio-util",
+ "tracing",
 ]
 
 [[package]]
 name = "datafusion-bio-format-vcf"
 version = "0.1.0"
-source = "git+https://github.com/biodatageeks/datafusion-bio-formats.git?rev=0b9746c77aeb0e3a29f6460cb29f48aa17625c1d#0b9746c77aeb0e3a29f6460cb29f48aa17625c1d"
+source = "git+https://github.com/biodatageeks/datafusion-bio-formats.git?rev=aecd7b316c1c498bff14c2cbb4ac0bd04d21612f#aecd7b316c1c498bff14c2cbb4ac0bd04d21612f"
 dependencies = [
  "async-compression",
  "async-stream",
@@ -3627,9 +3630,9 @@ dependencies = [
 [[package]]
 name = "noodles"
 version = "0.100.0"
-source = "git+https://github.com/biodatageeks/noodles.git?rev=289ef32e7d43d142914fb3f02335044ae293871c#289ef32e7d43d142914fb3f02335044ae293871c"
+source = "git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c#9b7b2c5b6531373918302d4c07410e583f1b5b5c"
 dependencies = [
- "noodles-bgzf 0.42.0",
+ "noodles-bgzf 0.42.0 (git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c)",
  "noodles-vcf 0.80.0",
 ]
 
@@ -3741,6 +3744,16 @@ dependencies = [
 name = "noodles-bgzf"
 version = "0.42.0"
 source = "git+https://github.com/biodatageeks/noodles.git?rev=289ef32e7d43d142914fb3f02335044ae293871c#289ef32e7d43d142914fb3f02335044ae293871c"
+dependencies = [
+ "bytes",
+ "crossbeam-channel",
+ "flate2",
+]
+
+[[package]]
+name = "noodles-bgzf"
+version = "0.42.0"
+source = "git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c#9b7b2c5b6531373918302d4c07410e583f1b5b5c"
 dependencies = [
  "bytes",
  "crossbeam-channel",
@@ -3777,6 +3790,14 @@ dependencies = [
  "bstr",
 ]
 
+[[package]]
+name = "noodles-core"
+version = "0.18.0"
+source = "git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c#9b7b2c5b6531373918302d4c07410e583f1b5b5c"
+dependencies = [
+ "bstr",
+]
+
 [[package]]
 name = "noodles-cram"
 version = "0.79.0"
@@ -3833,13 +3854,13 @@ dependencies = [
 [[package]]
 name = "noodles-csi"
 version = "0.50.0"
-source = "git+https://github.com/biodatageeks/noodles.git?rev=289ef32e7d43d142914fb3f02335044ae293871c#289ef32e7d43d142914fb3f02335044ae293871c"
+source = "git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c#9b7b2c5b6531373918302d4c07410e583f1b5b5c"
 dependencies = [
  "bit-vec",
  "bstr",
  "indexmap",
- "noodles-bgzf 0.42.0",
- "noodles-core 0.18.0",
+ "noodles-bgzf 0.42.0 (git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c)",
+ "noodles-core 0.18.0 (git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c)",
 ]
 
 [[package]]
@@ -3865,8 +3886,8 @@ dependencies = [
  "bytes",
  "futures",
  "memchr",
- "noodles-bgzf 0.42.0",
- "noodles-core 0.18.0",
+ "noodles-bgzf 0.42.0 (git+https://github.com/biodatageeks/noodles.git?rev=289ef32e7d43d142914fb3f02335044ae293871c)",
+ "noodles-core 0.18.0 (git+https://github.com/biodatageeks/noodles.git?rev=289ef32e7d43d142914fb3f02335044ae293871c)",
  "tokio",
 ]
 
@@ -3911,17 +3932,18 @@ dependencies = [
 
 [[package]]
 name = "noodles-gff"
-version = "0.50.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c689769bddd0464a1db695aef1824754d910b81f3f1c4c74ff418c89426052a8"
+version = "0.51.0"
+source = "git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c#9b7b2c5b6531373918302d4c07410e583f1b5b5c"
 dependencies = [
  "bstr",
  "futures",
  "indexmap",
  "lexical-core",
- "noodles-bgzf 0.41.0",
- "noodles-core 0.17.0",
- "noodles-csi 0.49.0",
+ "log",
+ "memchr",
+ "noodles-bgzf 0.42.0 (git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c)",
+ "noodles-core 0.18.0 (git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c)",
+ "noodles-csi 0.50.0",
  "percent-encoding",
  "tokio",
 ]
@@ -3991,12 +4013,12 @@ dependencies = [
 [[package]]
 name = "noodles-tabix"
 version = "0.56.0"
-source = "git+https://github.com/biodatageeks/noodles.git?rev=289ef32e7d43d142914fb3f02335044ae293871c#289ef32e7d43d142914fb3f02335044ae293871c"
+source = "git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c#9b7b2c5b6531373918302d4c07410e583f1b5b5c"
 dependencies = [
  "bstr",
  "indexmap",
- "noodles-bgzf 0.42.0",
- "noodles-core 0.18.0",
+ "noodles-bgzf 0.42.0 (git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c)",
+ "noodles-core 0.18.0 (git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c)",
  "noodles-csi 0.50.0",
  "tokio",
 ]
@@ -4022,13 +4044,13 @@ dependencies = [
 [[package]]
 name = "noodles-vcf"
 version = "0.80.0"
-source = "git+https://github.com/biodatageeks/noodles.git?rev=289ef32e7d43d142914fb3f02335044ae293871c#289ef32e7d43d142914fb3f02335044ae293871c"
+source = "git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c#9b7b2c5b6531373918302d4c07410e583f1b5b5c"
 dependencies = [
  "futures",
  "indexmap",
  "memchr",
- "noodles-bgzf 0.42.0",
- "noodles-core 0.18.0",
+ "noodles-bgzf 0.42.0 (git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c)",
+ "noodles-core 0.18.0 (git+https://github.com/biodatageeks/noodles.git?rev=9b7b2c5b6531373918302d4c07410e583f1b5b5c)",
  "noodles-csi 0.50.0",
  "noodles-tabix 0.56.0",
  "percent-encoding",
@@ -5203,7 +5225,7 @@ dependencies = [
 
 [[package]]
 name = "polars_bio"
-version = "0.13.1"
+version = "0.14.0"
 dependencies = [
  "arrow",
  "arrow-array",

{polars_bio-0.13.1 → polars_bio-0.14.0}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "polars_bio"
-version = "0.13.1"
+version = "0.14.0"
 edition = "2021"
 readme = "README.md"
 
@@ -36,13 +36,13 @@ polars-arrow =  { git = "https://github.com/mwiewior/polars.git" , rev = "da42ae
 polars-python = { git = "https://github.com/mwiewior/polars.git" , rev = "da42ae21ca9c25bc14562e36e07cf02eafd620ee"}
 
 
-datafusion-bio-format-vcf = { git = "https://github.com/biodatageeks/datafusion-bio-formats.git", rev = "0b9746c77aeb0e3a29f6460cb29f48aa17625c1d" }
-datafusion-bio-format-core = { git = "https://github.com/biodatageeks/datafusion-bio-formats.git", rev = "0b9746c77aeb0e3a29f6460cb29f48aa17625c1d" }
-datafusion-bio-format-gff = { git = "https://github.com/biodatageeks/datafusion-bio-formats.git", rev = "0b9746c77aeb0e3a29f6460cb29f48aa17625c1d" }
-datafusion-bio-format-fastq = { git = "https://github.com/biodatageeks/datafusion-bio-formats.git", rev = "0b9746c77aeb0e3a29f6460cb29f48aa17625c1d" }
-datafusion-bio-format-bam = { git = "https://github.com/biodatageeks/datafusion-bio-formats.git", rev = "0b9746c77aeb0e3a29f6460cb29f48aa17625c1d" }
-datafusion-bio-format-bed = { git = "https://github.com/biodatageeks/datafusion-bio-formats.git", rev = "0b9746c77aeb0e3a29f6460cb29f48aa17625c1d" }
-datafusion-bio-format-fasta = { git = "https://github.com/biodatageeks/datafusion-bio-formats.git", rev = "0b9746c77aeb0e3a29f6460cb29f48aa17625c1d" }
+datafusion-bio-format-vcf = { git = "https://github.com/biodatageeks/datafusion-bio-formats.git", rev = "aecd7b316c1c498bff14c2cbb4ac0bd04d21612f" }
+datafusion-bio-format-core = { git = "https://github.com/biodatageeks/datafusion-bio-formats.git", rev = "aecd7b316c1c498bff14c2cbb4ac0bd04d21612f" }
+datafusion-bio-format-gff = { git = "https://github.com/biodatageeks/datafusion-bio-formats.git", rev = "aecd7b316c1c498bff14c2cbb4ac0bd04d21612f" }
+datafusion-bio-format-fastq = { git = "https://github.com/biodatageeks/datafusion-bio-formats.git", rev = "aecd7b316c1c498bff14c2cbb4ac0bd04d21612f" }
+datafusion-bio-format-bam = { git = "https://github.com/biodatageeks/datafusion-bio-formats.git", rev = "aecd7b316c1c498bff14c2cbb4ac0bd04d21612f" }
+datafusion-bio-format-bed = { git = "https://github.com/biodatageeks/datafusion-bio-formats.git", rev = "aecd7b316c1c498bff14c2cbb4ac0bd04d21612f" }
+datafusion-bio-format-fasta = { git = "https://github.com/biodatageeks/datafusion-bio-formats.git", rev = "aecd7b316c1c498bff14c2cbb4ac0bd04d21612f" }
 
 
 

{polars_bio-0.13.1 → polars_bio-0.14.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: polars-bio
-Version: 0.13.1
+Version: 0.14.0
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -9,6 +9,7 @@ Requires-Dist: pyarrow~=21.0.0
 Requires-Dist: datafusion~=48.0.0
 Requires-Dist: tqdm~=4.67.1
 Requires-Dist: typing-extensions~=4.14.0
+Requires-Dist: mkdocs-glightbox>=0.5.1,<0.6.0
 Requires-Dist: pandas ; extra == 'pandas'
 Requires-Dist: bioframe ; extra == 'viz'
 Requires-Dist: matplotlib ; extra == 'viz'

polars_bio-0.14.0/docs/blog/index.md

@@ -0,0 +1,2 @@
+# Blog
+

polars_bio-0.14.0/docs/blog/posts/benchmark-operations-2025-09.md

@@ -0,0 +1,114 @@
+---
+draft: false
+date:
+  created: 2025-09-05
+  updated: 2025-09-05
+categories:
+  - performance
+  - benchmarks
+
+---
+
+# Interval operations benchmark — update September 2025
+
+## Introduction
+Benchmarking isn’t a one-and-done exercise—it’s a moving target. As tools evolve, new versions can shift performance profiles in meaningful ways, so keeping results current is just as important as the first round of measurements.
+
+Recently, three novel libraries that have started to gain traction: [pyranges1](https://github.com/pyranges/pyranges_1.x), [GenomicRanges](https://github.com/BiocPy/GenomicRanges) and [polars-bio](https://github.com/biodatageeks/polars-bio)
+![star-history-202595.png](figures/benchmark-sep-2025/star-history-202595.png)
+
+shipped major updates:
+
+* [pyranges1](https://github.com/pyranges/pyranges_1.x) adopted a new Rust backend ([ruranges](https://github.com/pyranges/ruranges)),
+* [GenomicRanges](https://github.com/BiocPy/GenomicRanges) switched its interval core to a Nested Containment List ([NCLS](https://github.com/pyranges/ncls)) and added multithreaded execution,
+* polars-bio migrated to the new Polars streaming engine and added support for new interval data structures. As of version `0.12.0` it supports:
+    * [COITrees](https://github.com/dcjones/coitrees)
+    * [IITree](https://github.com/rust-bio/rust-bio/blob/master/src/data_structures/interval_tree/array_backed_interval_tree.rs)
+    * [AVL-tree](https://github.com/rust-bio/rust-bio/blob/master/src/data_structures/interval_tree/avl_interval_tree.rs)
+    * [rust-lapper](https://github.com/sstadick/rust-lapper)
+    * [superintervals](https://github.com/kcleal/superintervals/)
+
+Each of these changes has the potential to meaningfully alter performance and memory characteristics for common genomic interval tasks.
+
+In this post, we revisit our benchmarks with those releases in mind. We focus on three everyday operations:
+
+* overlap detection,
+* nearest feature queries
+* overlap counting.
+
+For comparability, we use the same [AIList](/polars-bio/supplement/#real-dataset) dataset from our previous write-up, so you can see exactly how the new backends and data structures change the picture. Let’s dive in and see what’s faster, what’s leaner, and where the trade-offs now live.
+
+## Setup
+
+### Benchmark test cases
+
+| Dataset pairs | Size   | # of overlaps (1-based) |
+|---------------|--------|-------------------------|
+| 1-2 & 2-1     | Small  | 54,246                  |
+| 7-3 & 3-7     | Medium | 4,408,383               |
+| 8-7 & 7-8     | Large  | 307,184,634             |
+
+
+
+### Software versions
+
+| Library            | Version    |
+|--------------------|------------|
+| polars_bio         | 0.13.1     |
+| pyranges          | 0.1.14     |
+| genomicranges     | 0.7.2      |
+
+## Results
+
+### polars-bio interval data structures performance comparison
+![combined_multi_testcase.png](figures/benchmark-sep-2025/combined_multi_testcase.png){.glightbox}
+
+Key takeaways:
+
+- **Superintervals** seems to be the best default. Across all three test cases, it is consistently the fastest or tied for fastest, delivering 1.25–1.44x speedups over the **polars-bio default (COITrees)** and avoiding worst‑case behavior.
+- Lapper caveat: performs well on 1‑2 and 8‑7, but collapses on 7‑3 (≈25x slower than default), so it’s risky as a general‑purpose algorithm.
+- Intervaltree/Arrayintervaltree: reliable but slower. They trail superintervals by 20–70% depending on the case.
+
+
+### All operations comparison
+![all_operations_walltime_comparison.png](figures/benchmark-sep-2025/all_operations_walltime_comparison.png){.glightbox}
+
+![bench-20250-all_operations_speedup_comparison.png](figures/benchmark-sep-2025/bench-20250-all_operations_speedup_comparison.png){.glightbox}
+
+Key takeaways:
+
+- *Overlap*: **GenomicRanges** wins on small inputs (1‑2, 2‑1) by ~2.1–2.3x, but polars‑bio takes over from medium size onward and dominates on large (7‑8, 8‑7), where PyRanges falls far behind. Interesting case of *7-8* vs *8-7* when swapping inputs can significantly affect performance of GenomicRanges.
+- *Nearest*: **polars‑bio** leads decisively at every size; speedups over the others grow with input size (orders of magnitude on large datasets).
+- *Count overlaps*: **GenomicRanges** edges out polars‑bio on the smallest inputs, while **polars‑bio** is faster on medium and substantially faster on large inputs.
+
+### All operations parallel execution
+![benchmark_comparison_genomicranges_vs_polars_bio.png](figures/benchmark-sep-2025/benchmark_comparison_genomicranges_vs_polars_bio.png){.glightbox}
+
+![benchmark_speedup_comparison_genomicranges_vs_polars_bio.png](figures/benchmark-sep-2025/benchmark_speedup_comparison_genomicranges_vs_polars_bio.png){.glightbox}
+
+Key takeaways:
+
+- Thread scaling: **both** libraries (GenomicRanges and polars-bio) benefit from additional threads, but the absolute gap favors **polars‑bio** for medium/large datasets across overlap, nearest, and count overlaps.
+- Small overlaps: **GenomicRanges** remains >2x faster at 1–8 threads; on medium/large pairs its relative speed drops below 1x.
+- Nearest: **polars‑bio** stays on the 1x reference line; **GenomicRanges** is typically 10–100x slower (log scale) even with more threads.
+- Count overlaps: small inputs slightly favor **GenomicRanges**; for larger inputs **polars‑bio** maintains 2–10x advantage with stable scaling.
+
+### End to-end data proecesing
+
+Here we compare end-to-end performance including data loading, overlap operation, and saving results to CSV.
+
+!!! info
+     1. `POLARS_MAX_THREADS=1` was set to ensure fair comparison with single-threaded PyRanges.
+     2. Since GenomicRanges supports Polars DataFrames as input and output, we used them instead of Pandas to again ensure fair comparison with polars-bio.
+     3. GenomicRanges [find_overlaps](https://biocpy.github.io/GenomicRanges/api/genomicranges.html#genomicranges.GenomicRanges.GenomicRanges.find_overlaps) method returns hits-only table (indices of genomic intervals instead of genomic coordinates), we also benchmarked an extended version with additional lookup of intervals (`full rows`, [code](https://github.com/biodatageeks/polars-bio-bench/blob/master/src/utils.py#L99)) for fair comparison.
+
+![combined_benchmark_visualization.png](figures/benchmark-sep-2025/combined_benchmark_visualization.png){.glightbox}
+
+Key takeaways:
+
+- Wall time: **GenomicRanges (hits‑only)** is the fastest end‑to‑end here (~1.16x vs polars_bio) by avoiding full materialization of genomic intervals (unlike PyRanges and polars-bio that return pairs of genomic interval coordinates for each overlap); **PyRanges** is far slower; **GenomicRanges** (full rows, so with the output comparable with PyRanges and polars-bio) is much slower.
+- Memory: **polars-bio (streaming)** minimizes peak RAM (~0.7 GB) while keeping speed comparable to **polars-bio**. **GenomicRanges** (full rows) peaks at ~40 GB; hits‑only sits in the middle (~8.2 GB) as it only returns DataFrame with pairs of indices not full genomic coordinates.
+
+## Summary
+
+For small and medium datasets, all tools perform well; at large scale, **polars-bio** excels with better scalability and memory efficiency, achieving an ultra‑low footprint in streaming mode.

{polars_bio-0.13.1 → polars_bio-0.14.0}/docs/faq.md

@@ -18,6 +18,10 @@ polars-bio-intel kernel: [ 1611.175045] traps: python[8844] trap invalid opcode
 ```bash
 MKDOCS_EXPORTER_PDF=false JUPYTER_PLATFORM_DIRS=1 mkdocs serve  -w polars_bio
 ```
+Some pages of the documentation take a while to build—to speed up the process, you can disable dynamic content rendering:
+```bash
+MKDOCS_EXPORTER_PDF=false ENABLE_MD_EXEC=false ENABLE_MKDOCSTRINGS=false ENABLE_JUPYTER=false JUPYTER_PLATFORM_DIRS=1 mkdocs serve
+```
 
 4. How to build the source code and install in the current virtual environment?
 ```bash

{polars_bio-0.13.1 → polars_bio-0.14.0}/docs/supplement.md

@@ -51,7 +51,7 @@ The basic concept is that each operation consists of two sides: the **probe** si
     * [IITree](https://github.com/rust-bio/rust-bio/blob/master/src/data_structures/interval_tree/array_backed_interval_tree.rs)
     * [AVL-tree](https://github.com/rust-bio/rust-bio/blob/master/src/data_structures/interval_tree/avl_interval_tree.rs)
     * [rust-lapper](https://github.com/sstadick/rust-lapper)
-    * [superintervals](https://github.com/kcleal/superintervals/) - on the roadmap, see [issue](https://github.com/biodatageeks/polars-bio/issues/126)
+    * [superintervals](https://github.com/kcleal/superintervals/) - available since `polars-bio` version `0.12.0`
 Once the **build** side data structure is ready, then records from the **probe** side are processed against the search structure organized as record batches. Each record batch can be processed independently. Search structure nodes contains identifiers of the rows from the **build** side that are then used to construct a new record that is returned as a result of the operation.
 
 ### Out-of-core (streaming) processing

{polars_bio-0.13.1 → polars_bio-0.14.0}/mkdocs.yml

@@ -14,6 +14,7 @@ nav:
       - 🔬 Supplementary material: supplement.md
       - 📡 Contact: contact.md
 
+
   - Quick start: quickstart.md
   - Features: features.md
   - Tutorial: notebooks/tutorial.ipynb
@@ -22,20 +23,29 @@ nav:
   - FAQ: faq.md
   - 🔬 Supplementary material: supplement.md
   - Contact: contact.md
+  - 📖 Blog:
+      - blog/index.md
 
 plugins:
+  - blog:
+      post_date_format: full
+      archive: false
+      post_readtime: true
   - social
   - search
   - autorefs
   - mkdocs-jupyter:
+      enabled: !ENV [ENABLE_JUPYTER, true]
       execute: false
       allow_errors: false
   - mkdocstrings:
+      enabled: !ENV [ENABLE_MKDOCSTRINGS, true]
       default_handler: python
       handlers:
           options:
             docstring_style: google
-  - markdown-exec
+  - markdown-exec:
+      enabled: !ENV [ENABLE_MD_EXEC, true]
   - table-reader
   - mkdocs_matplotlib
   - exporter:
@@ -52,6 +62,8 @@ plugins:
             enabled: true
             output: .well-known/site.pdf
             covers: all
+  # Place glightbox last so it runs after other plugins
+  - glightbox
 theme:
   name: material
   logo: assets/logo.png
@@ -91,6 +103,7 @@ extra:
 
 markdown_extensions:
   - admonition
+  - codehilite
   - footnotes
   - pymdownx.critic
   - pymdownx.caret
@@ -123,4 +136,4 @@ markdown_extensions:
           format: !!python/name:pymdownx.superfences.fence_code_format
   - markdown.extensions.toc:
       baselevel: 1
-      permalink: ""
+      permalink: ""